General Transportation
Japanese public transportation system is very great. We prefer traveling by train, especially Shinkansen 新幹線 (bullet train), since we can enjoy the scenery while sitting comfortably. One of our favorite things to do is to buy some bentos and drinks from the train station and enjoy them on the shinkansen while looking outside through the windows. There are also a lot of domestic flight options if you want to travel by air. Since I mainly use trains, my posts will be focusing on trains with other modes of transportation mentioned as well.
Train system is very good in Japan and super reliable. I would suggest downloading some apps that are preloaded with the train maps offline, or getting familiar with map apps like Google Maps or Maps for directions. The map apps are so good now that not only do they tell you the mode of transportation (i.e., walk, type of train/bus) and estimated time of arrival, they even tell you the timetables, which door is closest to your exit, and whether your IC card has sufficient funds for this itinerary (this function shows up when you have the IC card on your Apple Wallet - for iPhone users). If you prefer paper maps, most train stations and airports (especially Information Booths) have them available for travelers. These are helpful when you are asking for directions so both you and the staff can draw on the map.
Services provided by the taxi drivers are amazing. They always make sure they handle your luggage with care (they even wear white gloves!). They are courteous and helpful, especially when you cannot speak Japanese, they will try their best to make sure they understand where you want to go to. The only downside is that it can be expensive. Our recent trip from Haneda International Airport (HND) to Shinjuku during peak hours was about 9500 jpy (at the time of writing this post, it’s about US $72) for 40 minutes of ride (due to traffic). In comparison, taking airport limousine bus would be around 1300 jpy (or US $10) per person.
Another point to note is that a normal sized taxi can fit two adults comfortably sitting in the back, one big luggage in the front passenger seat, and one big luggage and two small carry-ons in the trunk. Therefore, if you have more people and/or more luggage, you may need to get more taxi’s. I have been in bigger taxi before but since you usually get a taxi at the taxi stand, you have to take the next taxi available no matter what size it is.